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Van Duyne GD, Landy A. Bacteriophage lambda site-specific recombination. Mol Microbiol 2024; 121:895-911. [PMID: 38372210 PMCID: PMC11096046 DOI: 10.1111/mmi.15241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
The site-specific recombination pathway of bacteriophage λ encompasses isoenergetic but highly directional and tightly regulated integrative and excisive reactions that integrate and excise the vial chromosome into and out of the bacterial chromosome. The reactions require 240 bp of phage DNA and 21 bp of bacterial DNA comprising 16 protein binding sites that are differentially used in each pathway by the phage-encoded Int and Xis proteins and the host-encoded integration host factor and factor for inversion stimulation proteins. Structures of higher-order protein-DNA complexes of the four-way Holliday junction recombination intermediates provided clarifying insights into the mechanisms, directionality, and regulation of these two pathways, which are tightly linked to the physiology of the bacterial host cell. Here we review our current understanding of the mechanisms responsible for regulating and executing λ site-specific recombination, with an emphasis on key studies completed over the last decade.
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Affiliation(s)
- Gregory D Van Duyne
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arthur Landy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Warren Alpert Medical School, Brown University, Providence, Rhode Island, USA
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2
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Laanto E. Overcoming Bacteriophage Resistance in Phage Therapy. Methods Mol Biol 2024; 2738:401-410. [PMID: 37966611 DOI: 10.1007/978-1-0716-3549-0_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Antibiotic resistance among pathogenic bacteria is one of the most severe global challenges. It is predicted that over ten million lives will be lost annually by 2050. Phage therapy is a promising alternative to antibiotics. However, the ease of development of phage resistance during therapy is a concern. This review focuses on the possible ways to overcome phage resistance in phage therapy.
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Affiliation(s)
- Elina Laanto
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyväskylä, Finland.
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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3
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Nicolas AM, Sieradzki ET, Pett-Ridge J, Banfield JF, Taga ME, Firestone MK, Blazewicz SJ. A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil. Nat Commun 2023; 14:5835. [PMID: 37730729 PMCID: PMC10511743 DOI: 10.1038/s41467-023-40835-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/09/2023] [Indexed: 09/22/2023] Open
Abstract
Viruses are abundant, ubiquitous members of soil communities that kill microbial cells, but how they respond to perturbation of soil ecosystems is essentially unknown. Here, we investigate lineage-specific virus-host dynamics in grassland soil following "wet-up", when resident microbes are both resuscitated and lysed after a prolonged dry period. Quantitative isotope tracing, time-resolved metagenomics and viromic analyses indicate that dry soil holds a diverse but low biomass reservoir of virions, of which only a subset thrives following wet-up. Viral richness decreases by 50% within 24 h post wet-up, while viral biomass increases four-fold within one week. Though recent hypotheses suggest lysogeny predominates in soil, our evidence indicates that viruses in lytic cycles dominate the response to wet-up. We estimate that viruses drive a measurable and continuous rate of cell lysis, with up to 46% of microbial death driven by viral lysis one week following wet-up. Thus, viruses contribute to turnover of soil microbial biomass and the widely reported CO2 efflux following wet-up of seasonally dry soils.
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Affiliation(s)
- Alexa M Nicolas
- Plant & Microbial Biology Department, University of California Berkeley, Berkeley, CA, USA
| | - Ella T Sieradzki
- Environmental Science, Policy & Management Department, University of California Berkeley, Berkeley, CA, USA.
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA, USA
| | - Jillian F Banfield
- Environmental Science, Policy & Management Department, University of California Berkeley, Berkeley, CA, USA
- Earth and Planetary Sciences, University of California Berkeley, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michiko E Taga
- Plant & Microbial Biology Department, University of California Berkeley, Berkeley, CA, USA
| | - Mary K Firestone
- Environmental Science, Policy & Management Department, University of California Berkeley, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
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4
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Loganathan K, Viswanathan B. Genome editing for phage design and uses for therapeutic applications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:203-224. [PMID: 37770172 DOI: 10.1016/bs.pmbts.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The over usage of antibiotics leads to antibiotic abuse which in turn eventually raises resistance mechanisms among wide range of pathogens. Due to lack of experimental data of efficacy of phages as potential antimicrobial and therapeutic agent and also more specific and cumbersome isolation process against specific pathogens makes it not so feasible technology to be looked as an alternative therapy. But, recent developments in genome editing techniques enables programmed nuclease enzymes that has effectively improvised our methodology to make accurate changes in the genomes of prokaryote as well as eukaryote cells. It is already strengthening our ability to improvise genetic engineering to disease identification by facilitating the creation of more precise models to identify the root cause. The present chapter discusses on improvisation of phage therapy using recent genome editing tools and also shares data on the methods of usage of phages and their derivatives like proteins and enzymes such as lysins and depolymerases, as a potential therapeutic or prophylaxis agent. Methods involved in recombinant based techniques were also discussed in this chapter. Combination of traditional approach with modern tools has led to a potential development of phage-based therapeutics in near future.
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5
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Sun Z, Yu T, Cao X, Gao L, Pang Q, Liu B, Deng H. Identification and characterization of Deoxyribonuclease II in planarian Dugesia japonica. Gene 2022; 826:146464. [PMID: 35358655 DOI: 10.1016/j.gene.2022.146464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/09/2022] [Accepted: 03/25/2022] [Indexed: 11/04/2022]
Abstract
Deoxyribonuclease II (DNase II) has been found to regulate inflammation, autoimmunity and apoptosis in vertebrates and invertebrates. The strong capacity of degrading DNA makes DNase II play an important role in the immune process. Planarian has become one of the model references due to its strong immune system, the environment they live makes planarians face the threat of microorganisms and injury, the strong immune system can protect planarians from the threat of bacterial and infection. In this study, we found that there was DNase in the lysis buffer of planarians, then we acquired the sequence of DjDN2s (Dugesia japonica DNase2s) and confirmed the DjDN2s were conserved DNase IIs. The predicted structure showed the active sites and binding patterns of DjDN2s. Whole-mount in situ hybridization results showed DjDN2s mainly expressed in immune organs. Quantitative real-time PCR revealed that the expression of DjDN2s upregulated in varying degrees when got hurt and challenged with bacteria, and the knockdown of DjDN2s led to the slower repair of wound. The recombinant phages which take DjDN2 also had the ability to degrade DNA and clear young biofilm of Gram-negative bacteria. Collectively, DNase II of planarian might play a role in the antimicrobial response and wound-induced response.
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Affiliation(s)
- Zhe Sun
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Tong Yu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Xiangyu Cao
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Lili Gao
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Qiuxiang Pang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China.
| | - Baohua Liu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China; Shenzhen University of Health Science Center, Shenzhen, Guangdong 518060, China.
| | - Hongkuan Deng
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China.
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6
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Paramasivam K, Shen Y, Yuan J, Waheed I, Mao C, Zhou X. Advances in the Development of Phage-Based Probes for Detection of Bio-Species. BIOSENSORS 2022; 12:30. [PMID: 35049658 PMCID: PMC8773867 DOI: 10.3390/bios12010030] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/27/2021] [Accepted: 01/04/2022] [Indexed: 05/10/2023]
Abstract
Bacteriophages, abbreviated as "phages", have been developed as emerging nanoprobes for the detection of a wide variety of biological species, such as biomarker molecules and pathogens. Nanosized phages can display a certain length of exogenous peptides of arbitrary sequence or single-chain variable fragments (scFv) of antibodies that specifically bind to the targets of interest, such as animal cells, bacteria, viruses, and protein molecules. Metal nanoparticles generally have unique plasmon resonance effects. Metal nanoparticles such as gold, silver, and magnetism are widely used in the field of visual detection. A phage can be assembled with metal nanoparticles to form an organic-inorganic hybrid probe due to its nanometer-scale size and excellent modifiability. Due to the unique plasmon resonance effect of this composite probe, this technology can be used to visually detect objects of interest under a dark-field microscope. In summary, this review summarizes the recent advances in the development of phage-based probes for ultra-sensitive detection of various bio-species, outlining the advantages and limitations of detection technology of phage-based assays, and highlighting the commonly used editing technologies of phage genomes such as homologous recombination and clustered regularly interspaced palindromic repeats/CRISPR-associated proteins system (CRISPR-Cas). Finally, we discuss the possible scenarios for clinical application of phage-probe-based detection methods.
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Affiliation(s)
- Kameshpandian Paramasivam
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (K.P.); (Y.S.); (J.Y.); (I.W.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Yuanzhao Shen
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (K.P.); (Y.S.); (J.Y.); (I.W.)
| | - Jiasheng Yuan
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (K.P.); (Y.S.); (J.Y.); (I.W.)
| | - Ibtesam Waheed
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (K.P.); (Y.S.); (J.Y.); (I.W.)
| | - Chuanbin Mao
- Stephenson Life Sciences Research Center, Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019-5300, USA;
| | - Xin Zhou
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (K.P.); (Y.S.); (J.Y.); (I.W.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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Omata K, Hibi N, Nakano S, Komoto S, Sato K, Nunokawa K, Amano S, Ueda K, Takano H. Distribution and genome structures of temperate phages in acetic acid bacteria. Sci Rep 2021; 11:21567. [PMID: 34732777 PMCID: PMC8566455 DOI: 10.1038/s41598-021-00998-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/19/2021] [Indexed: 01/21/2023] Open
Abstract
Acetic acid bacteria (AAB) are industrial microorganisms used for vinegar fermentation. Herein, we investigated the distribution and genome structures of mitomycin C-inducible temperate phages in AAB. Transmission electron microscopy analysis revealed phage-like particles in 15 out of a total 177 acetic acid bacterial strains, all of which showed morphology similar to myoviridae-type phage. The complete genome sequences of the six phages derived from three strains each of Acetobacter and Komagataeibacter strains were determined, harboring a genome size ranging from 34,100 to 53,798 bp. A phage AP1 from A. pasteurianus NBRC 109446 was predicted as an active phage based on the genomic information, and actually had the ability to infect its phiAP1-cured strain. The attachment sites for phiAP1 were located in the 3'-end region of the tRNAser gene. We also developed a chromosome-integrative vector, p2096int, based on the integrase function of phiAP1, and it was successfully integrated into the attachment site of the phiAP1-cured strain, which may be used as a valuable tool for the genetic engineering. Overall, this study showed the distribution of mitomycin C-inducible temperate phages in AAB, and identified the active temperate phage o f A. pasteurianus.
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Affiliation(s)
- Koki Omata
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | | | | | | | - Kazuki Sato
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Kei Nunokawa
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Shoichi Amano
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Kenji Ueda
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Hideaki Takano
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Kanagawa, Japan.
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8
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Chen Y, Batra H, Dong J, Chen C, Rao VB, Tao P. Genetic Engineering of Bacteriophages Against Infectious Diseases. Front Microbiol 2019; 10:954. [PMID: 31130936 PMCID: PMC6509161 DOI: 10.3389/fmicb.2019.00954] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/15/2019] [Indexed: 12/19/2022] Open
Abstract
Bacteriophages (phages) are the most abundant and widely distributed organisms on Earth, constituting a virtually unlimited resource to explore the development of biomedical therapies. The therapeutic use of phages to treat bacterial infections (“phage therapy”) was conceived by Felix d’Herelle nearly a century ago. However, its power has been realized only recently, largely due to the emergence of multi-antibiotic resistant bacterial pathogens. Progress in technologies, such as high-throughput sequencing, genome editing, and synthetic biology, further opened doors to explore this vast treasure trove. Here, we review some of the emerging themes on the use of phages against infectious diseases. In addition to phage therapy, phages have also been developed as vaccine platforms to deliver antigens as part of virus-like nanoparticles that can stimulate immune responses and prevent pathogen infections. Phage engineering promises to generate phage variants with unique properties for prophylactic and therapeutic applications. These approaches have created momentum to accelerate basic as well as translational phage research and potential development of therapeutics in the near future.
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Affiliation(s)
- Yibao Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Himanshu Batra
- Department of Biology, The Catholic University of America, Washington, DC, United States
| | - Junhua Dong
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Cen Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Venigalla B Rao
- Department of Biology, The Catholic University of America, Washington, DC, United States
| | - Pan Tao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China.,Department of Biology, The Catholic University of America, Washington, DC, United States
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9
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Lee J, Arun Kumar S, Jhan YY, Bishop CJ. Engineering DNA vaccines against infectious diseases. Acta Biomater 2018; 80:31-47. [PMID: 30172933 PMCID: PMC7105045 DOI: 10.1016/j.actbio.2018.08.033] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 08/14/2018] [Accepted: 08/23/2018] [Indexed: 12/30/2022]
Abstract
Engineering vaccine-based therapeutics for infectious diseases is highly challenging, as trial formulations are often found to be nonspecific, ineffective, thermally or hydrolytically unstable, and/or toxic. Vaccines have greatly improved the therapeutic landscape for treating infectious diseases and have significantly reduced the threat by therapeutic and preventative approaches. Furthermore, the advent of recombinant technologies has greatly facilitated growth within the vaccine realm by mitigating risks such as virulence reversion despite making the production processes more cumbersome. In addition, seroconversion can also be enhanced by recombinant technology through kinetic and nonkinetic approaches, which are discussed herein. Recombinant technologies have greatly improved both amino acid-based vaccines and DNA-based vaccines. A plateau of interest has been reached between 2001 and 2010 for the scientific community with regard to DNA vaccine endeavors. The decrease in interest may likely be attributed to difficulties in improving immunogenic properties associated with DNA vaccines, although there has been research demonstrating improvement and optimization to this end. Despite improvement, to the extent of our knowledge, there are currently no regulatory body-approved DNA vaccines for human use (four vaccines approved for animal use). This article discusses engineering DNA vaccines against infectious diseases while discussing advantages and disadvantages of each, with an emphasis on applications of these DNA vaccines. Statement of Significance This review paper summarizes the state of the engineered/recombinant DNA vaccine field, with a scope entailing “Engineering DNA vaccines against infectious diseases”. We endeavor to emphasize recent advances, recapitulating the current state of the field. In addition to discussing DNA therapeutics that have already been clinically translated, this review also examines current research developments, and the challenges thwarting further progression. Our review covers: recombinant DNA-based subunit vaccines; internalization and processing; enhancing immune protection via adjuvants; manufacturing and engineering DNA; the safety, stability and delivery of DNA vaccines or plasmids; controlling gene expression using plasmid engineering and gene circuits; overcoming immunogenic issues; and commercial successes. We hope that this review will inspire further research in DNA vaccine development.
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10
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Zhang S, Fan C, Xia Y, Li M, Wang Y, Cui X, Xiao W. Characterization of a novel bacteriophage specific to Exiguobacterium indicum isolated from a plateau eutrophic lake. J Basic Microbiol 2018; 59:206-214. [PMID: 30284309 DOI: 10.1002/jobm.201800184] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/18/2018] [Accepted: 09/11/2018] [Indexed: 12/19/2022]
Abstract
Exiguobacterium is a versatile genus with potential in industry and agriculture. No bacteriophage that infects Exiguobacterium has been reported, despite its potential impacts on the utilization of Exiguobacterium. E. indicum EI9 was isolated from Dianchi Lake, a plateau eutrophic lake in China, which can significantly inhibit the growth of Microcystis aeruginosa. To isolate and characterize Exiguobacterium-infecting bacteriophage, a virulent bacteriophage, DCEIV-9 that specifically infects E. indicum EI9 was isolated from Dianchi lake water sample. DCEIV-9 produced tiny, round, and clear plaques with 0.5-1 mm in diameter. Electron microscopy showed that DCEIV-9 is a typical representative of the Siphoviridae, with an icosahedral head (56 nm in diameter) and a non-contractile tail (163 nm in length). Based on a one-step growth curve, latent period of 20 min and burst size of 51 PFU/infected cell were determined. DCEIV-9 was sensitive to temperature over 50 °C and prefers acid environment. DCEIV-9 was extremely sensitive to proteinase K, chloroform, ethanol, Triton X-100 but not sensitive to SDS. Restriction endonucleases analysis indicated that DCEIV-9 is a dsDNA virus. DCEIV-9 can only infect E. indicum, indicates that it has a narrow host range. DCEIV-9 is a potential new species.
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Affiliation(s)
- Shiying Zhang
- Yunnan Engineering Laboratory of Soil Fertility and Pollution Remediation, Yunnan Agricultural University, Kunming, China.,Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming, China
| | - Cong Fan
- Yunnan Engineering Laboratory of Soil Fertility and Pollution Remediation, Yunnan Agricultural University, Kunming, China.,Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming, China
| | - Yunsheng Xia
- Yunnan Engineering Laboratory of Soil Fertility and Pollution Remediation, Yunnan Agricultural University, Kunming, China
| | - Mengke Li
- Yunnan Engineering Laboratory of Soil Fertility and Pollution Remediation, Yunnan Agricultural University, Kunming, China.,Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming, China
| | - Yongxia Wang
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Xiaolong Cui
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Wei Xiao
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
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11
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Kroth PG, Bones AM, Daboussi F, Ferrante MI, Jaubert M, Kolot M, Nymark M, Río Bártulos C, Ritter A, Russo MT, Serif M, Winge P, Falciatore A. Genome editing in diatoms: achievements and goals. PLANT CELL REPORTS 2018; 37:1401-1408. [PMID: 30167805 DOI: 10.1007/s00299-018-2334-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/07/2018] [Indexed: 05/20/2023]
Abstract
Diatoms are major components of phytoplankton and play a key role in the ecology of aquatic ecosystems. These algae are of great scientific importance for a wide variety of research areas, ranging from marine ecology and oceanography to biotechnology. During the last 20 years, the availability of genomic information on selected diatom species and a substantial progress in genetic manipulation, strongly contributed to establishing diatoms as molecular model organisms for marine biology research. Recently, tailored TALEN endonucleases and the CRISPR/Cas9 system were utilized in diatoms, allowing targeted genetic modifications and the generation of knockout strains. These approaches are extremely valuable for diatom research because breeding, forward genetic screens by random insertion, and chemical mutagenesis are not applicable to the available model species Phaeodactylum tricornutum and Thalassiosira pseudonana, which do not cross sexually in the lab. Here, we provide an overview of the genetic toolbox that is currently available for performing stable genetic modifications in diatoms. We also discuss novel challenges that need to be addressed to fully exploit the potential of these technologies for the characterization of diatom biology and for metabolic engineering.
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Affiliation(s)
- Peter G Kroth
- Fachbereich Biologie, Universität Konstanz, 78457, Konstanz, Germany.
| | - Atle M Bones
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Fayza Daboussi
- LISBP, Université de Toulouse, CNRS, INSA, 135 Avenue de Rangueil, 31077, Toulouse, France
| | - Maria I Ferrante
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
| | - Marianne Jaubert
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, 75005, Paris, France
| | - Misha Kolot
- Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
- Department of Biochemistry and Molecular Biology, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Marianne Nymark
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | | | - Andrés Ritter
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, 75005, Paris, France
| | - Monia T Russo
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
| | - Manuel Serif
- LISBP, Université de Toulouse, CNRS, INSA, 135 Avenue de Rangueil, 31077, Toulouse, France
| | - Per Winge
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Angela Falciatore
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, 75005, Paris, France.
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12
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Single-Homology-Arm Linear DNA Recombination by the Nonhomologous End Joining Pathway as a Novel and Simple Gene Inactivation Method: a Proof-of-Concept Study in Dietzia sp. Strain DQ12-45-1b. Appl Environ Microbiol 2018; 84:AEM.00795-18. [PMID: 30030230 DOI: 10.1128/aem.00795-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/04/2018] [Indexed: 02/06/2023] Open
Abstract
Nonhomologous end joining (NHEJ) is critical for genome stability because of its roles in double-strand break repair. Ku and ligase D (LigD) are the crucial proteins in this process, and strains expressing Ku and LigD can cyclize linear DNA in vivo Here, we established a proof-of-concept single-homology-arm linear DNA recombination for gene inactivation or genome editing by which cyclization of linear DNA in vivo by NHEJ could be used to generate nonreplicable circular DNA and could allow allelic exchanges between the circular DNA and the chromosome. We achieved this approach in Dietzia sp. strain DQ12-45-1b, which expresses Ku and LigD homologs and presents NHEJ activity. By transforming the strain with a linear DNA single homolog to the sequence in the chromosome, we mutated the genome. This method did not require the screening of suitable plasmids and was easy and time-effective. Bioinformatic analysis showed that more than 20% of prokaryotic organisms contain Ku and LigD, suggesting the wide distribution of NHEJ activities. Moreover, an Escherichia coli strain also showed NHEJ activity when the Ku and LigD of Dietzia sp. DQ12-45-1b were introduced and expressed in it. Therefore, this method may be a widely applicable genome editing tool for diverse prokaryotic organisms, especially for nonmodel microorganisms.IMPORTANCE Many nonmodel Gram-positive bacteria lack efficient genetic manipulation systems, but they express genes encoding Ku and LigD. The NHEJ pathway in Dietzia sp. DQ12-45-1b was evaluated and was used to successfully knock out 11 genes in the genome. Since bioinformatic studies revealed that the putative genes encoding Ku and LigD ubiquitously exist in phylogenetically diverse bacteria and archaea, the single-homology-arm linear DNA recombination by the NHEJ pathway could be a potentially applicable genetic manipulation method for diverse nonmodel prokaryotic organisms.
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13
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Elias A, Gritsenko N, Gorovits R, Spector I, Prag G, Yagil E, Kolot M. Anti-cancer binary system activated by bacteriophage HK022 integrase. Oncotarget 2018; 9:27487-27501. [PMID: 29938000 PMCID: PMC6007955 DOI: 10.18632/oncotarget.25512] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 05/14/2018] [Indexed: 01/10/2023] Open
Abstract
The binary system presented in this work is based on the bacteriophage HK022 integrase recombinase that activates the expression of a silenced Diphtheria toxin gene, both controlled by the cancer specific hTERT promoter. Using a lung cancer mice model, assays of different apoptotic and anti-apoptotic factors have demonstrated that the Integrase based binary system is highly specific towards cancer cells and more efficient compared to the conventional mono system whose toxin is directly expressed under hTERT. In a mice survival test, this binary system demonstrated longer persistence compared to the untreated and the mono treated ones. The reason underlying the advantage of this binary system over the mono system seems to be an overexpression of various hTERT suppressing factors induced by the mono system.
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Affiliation(s)
- Amer Elias
- Department of Biochemistry and Molecular Biology, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Natasha Gritsenko
- Department of Biochemistry and Molecular Biology, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Rena Gorovits
- Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Itay Spector
- Department of Biochemistry and Molecular Biology, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Gali Prag
- Department of Biochemistry and Molecular Biology, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Ezra Yagil
- Department of Biochemistry and Molecular Biology, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Mikhail Kolot
- Department of Biochemistry and Molecular Biology, Tel-Aviv University, Tel-Aviv 69978, Israel
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Rashid SJ, Barylski J, Hargreaves KR, Millard AA, Vinner GK, Clokie MRJ. Two Novel Myoviruses from the North of Iraq Reveal Insights into Clostridium difficile Phage Diversity and Biology. Viruses 2016; 8:v8110310. [PMID: 27854339 PMCID: PMC5127024 DOI: 10.3390/v8110310] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/03/2016] [Accepted: 11/08/2016] [Indexed: 12/18/2022] Open
Abstract
Bacteriophages (phages) are increasingly being explored as therapeutic agents to combat bacterial diseases, including Clostridium difficile infections. Therapeutic phages need to be able to efficiently target and kill a wide range of clinically relevant strains. While many phage groups have yet to be investigated in detail, those with new and useful properties can potentially be identified when phages from newly studied geographies are characterised. Here, we report the isolation of C. difficile phages from soil samples from the north of Iraq. Two myoviruses, CDKM15 and CDKM9, were selected for detailed sequence analysis on the basis of their broad and potentially useful host range. CDKM9 infects 25/80 strains from 12/20 C. difficile ribotypes, and CDKM15 infects 20/80 strains from 9/20 ribotypes. Both phages can infect the clinically relevant ribotypes R027 and R001. Phylogenetic analysis based on whole genome sequencing revealed that the phages are genetically distinct from each other but closely related to other long-tailed myoviruses. A comparative genomic analysis revealed key differences in the genes predicted to encode for proteins involved in bacterial infection. Notably, CDKM15 carries a clustered regularly interspaced short palindromic repeat (CRISPR) array with spacers that are homologous to sequences in the CDKM9 genome and of phages from diverse localities. The findings presented suggest a possible shared evolutionary past for these phages and provides evidence of their widespread dispersal.
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Affiliation(s)
- Srwa J Rashid
- Department of Infection, Immunity and Inflammation, Medical Sciences Building, University of Leicester, University Road, Leicester, LE1 9HN, UK.
| | - Jakub Barylski
- Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan 61-712, Poland.
| | | | - Andrew A Millard
- Microbiology & Infection Unit, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.
| | - Gurinder K Vinner
- Department of Chemical Engineering, Loughborough University, Loughborough, LE11 3TU, UK.
| | - Martha R J Clokie
- Department of Infection, Immunity and Inflammation, Medical Sciences Building, University of Leicester, University Road, Leicester, LE1 9HN, UK.
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15
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crAssphage is not associated with diarrhoea and has high genetic diversity. Epidemiol Infect 2016; 144:3549-3553. [DOI: 10.1017/s095026881600176x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
SUMMARYcrAssphage is a newly discovered gut bacteriophage. However, its pathogenicity and molecular epidemiology in humans are as yet unclear. In this study, we investigated the association between crAssphage and diarrhoea, as well as the molecular epidemiology of crAssphage in Chinese patients from our hospital. Our results indicated that there were no significant differences in the crAssphage-positive ratio and viral loads in faecal supernatants between adults with diarrhoea and healthy adults. Of infants and children with diarrhoea, 2·8% were found to be crAssphage-positive, including two infants aged <1 month. Markedly, of all confirmed crAssphage-positive strains, 100% had the ORF00039 deletion and 77·8% had low identity of ORF00018 compared to crAssphage (GenBank accession no. NC_024711, designated genotype 1). Thus, crAssphage was not associated with diarrhoea and most strains of crAssphage in Chinese patients (designated genotype 2) were characterized by the ORF00039 deletion and low identity of ORF00018.
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16
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Uchiyama J, Takemura-Uchiyama I, Kato SI, Takeuchi H, Sakaguchi Y, Ujihara T, Daibata M, Shimakura H, Okamoto N, Sakaguchi M, Matsuzaki S. Screening of KHP30-like prophages among Japanese Helicobacter pylori strains, and genetic analysis of a defective KHP30-like prophage sequence integrated in the genome of the H. pylori strain NY40. FEMS Microbiol Lett 2016; 363:fnw157. [PMID: 27388014 DOI: 10.1093/femsle/fnw157] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2016] [Indexed: 12/11/2022] Open
Abstract
We have recently reported the active Helicobacter pylori bacteriophages (phages), KHP30 and KHP40, the genomic DNAs of which exist as episomes in host bacterial strains isolated in Japan (i.e. pseudolysogeny). In this study, we examined the possibility of the lysogeny of active KHP30-like phages in Japanese H. pylori strains, because their genomes contain a putative integrase gene. Only the NY40 strain yielded partial detection of a KHP30-like prophage sequence in PCR among 174 Japanese H. pylori isolates, except for strains producing the above active phages. Next, according to the genomic analysis of the NY40 strain, the KHP30-like prophage sequence was found to be located from ca. 524 to 549 kb in the host chromosome. The attachment sites, attL and attR, in the NY40 genome showed almost the same genomic location and sequence as those detected in a French isolate B38, suggesting that an active parental KHP30-like phage had integrated into the ancestral NY40 genome in a site-specific manner. The prophage found in the NY40 genome was assumed to have been genetically modified, after site-specific integration. These, together with the data in the KHP30-like prophages of other H. pylori genomes, suggest that the lysogenic state of the KHP30-like phages is generally unstable.
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Affiliation(s)
- Jumpei Uchiyama
- Department of Veterinary Microbiology, School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Iyo Takemura-Uchiyama
- Department of Veterinary Microbiology, School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Shin-Ichiro Kato
- Research Institute of Molecular Genetics, Kochi University, Kochi 783-8502, Japan
| | - Hiroaki Takeuchi
- Department of Clinical Laboratory Medicine, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
| | - Yoshihiko Sakaguchi
- Department of Microbiology, Kitasato University School of Medicine, Kanagawa 252-0374, Japan
| | - Takako Ujihara
- Science Research Center, Kochi University, Kochi 783-8505, Japan
| | - Masanori Daibata
- Department of Microbiology and Infection, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
| | - Hidekatsu Shimakura
- Department of Veterinary Microbiology, School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Noriaki Okamoto
- Department of Veterinary Microbiology, School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Masahiro Sakaguchi
- Department of Veterinary Microbiology, School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Shigenobu Matsuzaki
- Department of Microbiology and Infection, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
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17
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Huang Y, Liu Z, Rong YS. Genome Editing: From Drosophila to Non-Model Insects and Beyond. J Genet Genomics 2016; 43:263-72. [PMID: 27216295 DOI: 10.1016/j.jgg.2016.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 04/06/2016] [Accepted: 04/20/2016] [Indexed: 12/21/2022]
Abstract
Insect is the largest group of animals on land. Many insect species inflict economical and health losses to humans. Yet many more benefit us by helping to maintain balances in our ecosystem. The benefits that insects offer remain largely untapped, justifying our continuing efforts to develop tools to better understand their biology and to better manage their activities. Here we focus on reviewing the progresses made in the development of genome engineering tools for model insects. Instead of detailed descriptions of the molecular mechanisms underlying each technical advance, we focus our discussion on the logistics for implementing similar tools in non-model insects. Since none of the tools were developed specific for insects, similar approaches can be applied to other non-model organisms.
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Affiliation(s)
- Yueping Huang
- Institute of Entomology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhiping Liu
- Institute of Entomology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yikang S Rong
- Institute of Entomology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.
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18
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Cancer-specific binary expression system activated in mice by bacteriophage HK022 Integrase. Sci Rep 2016; 6:24971. [PMID: 27117628 PMCID: PMC4846993 DOI: 10.1038/srep24971] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/07/2016] [Indexed: 12/01/2022] Open
Abstract
Binary systems based on site-specific recombination have been used for tumor specific transcription targeting of suicide genes in animal models. In these binary systems a site specific recombinase or integrase that is expressed from a tumor specific promoter drives tumor specific expression of a cytotoxic gene. In the present study we developed a new cancer specific binary expression system activated by the Integrase (Int) of the lambdoid phage HK022. We demonstrate the validity of this system by the specific expression of a luciferase (luc) reporter in human embryonic kidney 293T (HEK293T) cells and in a lung cancer mouse model. Due to the absence viral vectors and of cytotoxicity the Int based binary system offers advantages over previously described counterparts and may therefore be developed into a safer cancer cell killing system.
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19
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Weissman KJ. Genetic engineering of modular PKSs: from combinatorial biosynthesis to synthetic biology. Nat Prod Rep 2016; 33:203-30. [DOI: 10.1039/c5np00109a] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This reviews covers on-going efforts at engineering the gigantic modular polyketide synthases (PKSs), highlighting both notable successes and failures.
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Affiliation(s)
- Kira J. Weissman
- UMR 7365
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA)
- CNRS-Université de Lorraine
- Biopôle de l'Université de Lorraine
- 54505 Vandœuvre-lès-Nancy Cedex
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20
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Foldvari M, Chen DW, Nafissi N, Calderon D, Narsineni L, Rafiee A. Non-viral gene therapy: Gains and challenges of non-invasive administration methods. J Control Release 2015; 240:165-190. [PMID: 26686079 DOI: 10.1016/j.jconrel.2015.12.012] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 11/26/2015] [Accepted: 12/09/2015] [Indexed: 12/20/2022]
Abstract
Gene therapy is becoming an influential part of the rapidly increasing armamentarium of biopharmaceuticals for improving health and combating diseases. Currently, three gene therapy treatments are approved by regulatory agencies. While these treatments utilize viral vectors, non-viral alternative technologies are also being developed to improve the safety profile and manufacturability of gene carrier formulations. We present an overview of gene-based therapies focusing on non-viral gene delivery systems and the genetic therapeutic tools that will further revolutionize medical treatment with primary focus on the range and development of non-invasive delivery systems for dermal, transdermal, ocular and pulmonary administrations and perspectives on other administration methods such as intranasal, oral, buccal, vaginal, rectal and otic delivery.
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Affiliation(s)
- Marianna Foldvari
- School of Pharmacy, Waterloo Institute of Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada; Center for Bioengineering and Biotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada.
| | - Ding Wen Chen
- School of Pharmacy, Waterloo Institute of Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada; Center for Bioengineering and Biotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Nafiseh Nafissi
- School of Pharmacy, Waterloo Institute of Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada; Center for Bioengineering and Biotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Daniella Calderon
- School of Pharmacy, Waterloo Institute of Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada; Center for Bioengineering and Biotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Lokesh Narsineni
- School of Pharmacy, Waterloo Institute of Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada; Center for Bioengineering and Biotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Amirreza Rafiee
- School of Pharmacy, Waterloo Institute of Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada; Center for Bioengineering and Biotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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21
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Nafissi N, Foldvari M. Neuroprotective therapies in glaucoma: II. Genetic nanotechnology tools. Front Neurosci 2015; 9:355. [PMID: 26528114 PMCID: PMC4604245 DOI: 10.3389/fnins.2015.00355] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/17/2015] [Indexed: 01/01/2023] Open
Abstract
Neurotrophic factor genome engineering could have many potential applications not only in the deeper understanding of neurodegenerative disorders but also in improved therapeutics. The fields of nanomedicine, regenerative medicine, and gene/cell-based therapy have been revolutionized by the development of safer and efficient non-viral technologies for gene delivery and genome editing with modern techniques for insertion of the neurotrophic factors into clinically relevant cells for a more sustained pharmaceutical effect. It has been suggested that the long-term expression of neurotrophic factors is the ultimate approach to prevent and/or treat neurodegenerative disorders such as glaucoma in patients who do not respond to available treatments or are at the progressive stage of the disease. Recent preclinical research suggests that novel neuroprotective gene and cell therapeutics could be promising approaches for both non-invasive neuroprotection and regenerative functions in the eye. Several progenitor and retinal cell types have been investigated as potential candidates for glaucoma neurotrophin therapy either as targets for gene therapy, options for cell replacement therapy, or as vehicles for gene delivery. Therefore, in parallel with deeper understanding of the specific protective effects of different neurotrophic factors and the potential therapeutic cell candidates for glaucoma neuroprotection, the development of non-invasive and highly specific gene delivery methods with safe and effective technologies to modify cell candidates for life-long neuroprotection in the eye is essential before investing in this field.
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Affiliation(s)
| | - Marianna Foldvari
- School of Pharmacy and Waterloo Institute of Nanotechnology, University of WaterlooWaterloo, ON, Canada
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22
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Cheepudom J, Lee CC, Cai B, Meng M. Isolation, characterization, and complete genome analysis of P1312, a thermostable bacteriophage that infects Thermobifida fusca. Front Microbiol 2015; 6:959. [PMID: 26441893 PMCID: PMC4569894 DOI: 10.3389/fmicb.2015.00959] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/31/2015] [Indexed: 11/13/2022] Open
Abstract
Thermobifida fusca is a moderately thermophilic and cellulolytic actinobacterium. It is of particular interest due to its ability to not only produce a variety of biotechnologically relevant enzymes but also serve as an alternative host for metabolic engineering for the production of valuable chemicals from lignocellulosic agricultural wastes. No bacteriophage that infects T. fusca has been reported, despite its potential impacts on the utilization of T. fusca. In this study, an extremely thermostable bacteriophage P1312 that infects T. fusca was isolated from manure compost. Electron microscopy showed that P1312 has an icosahedral head and a long flexible non-contractile tail, a characteristic of the family Siphoviridae. P1312 has a double-stranded DNA genome of 60,284 bp with 93 potential ORFs. Thirty-one ORFs encode proteins having putative biological functions. The genes involved in phage particle formation cluster together in a region of approximately 16 kb, followed by a segment containing genes presumably for DNA degradation/modification and cell wall disruption. The genes required for DNA replication and transcriptional control are dispersed within the rest of the genome. Phylogenetic analysis of large terminase subunit suggests that P1312 is a headful packaging phage containing a chromosome with circularly permuted direct terminal repeats.
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Affiliation(s)
- Jatuporn Cheepudom
- Graduate Institute of Biotechnology, National Chung Hsing University Taichung, Taiwan
| | - Cheng-Cheng Lee
- Graduate Institute of Biotechnology, National Chung Hsing University Taichung, Taiwan
| | - Bingfu Cai
- Graduate Institute of Biotechnology, National Chung Hsing University Taichung, Taiwan
| | - Menghsiao Meng
- Graduate Institute of Biotechnology, National Chung Hsing University Taichung, Taiwan
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23
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Nafissi N, Foldvari M. Neuroprotective therapies in glaucoma: I. Neurotrophic factor delivery. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2015; 8:240-54. [PMID: 26306832 DOI: 10.1002/wnan.1361] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 06/15/2015] [Accepted: 07/04/2015] [Indexed: 12/11/2022]
Abstract
Glaucoma is a neurodegenerative eye disease that causes permanent blindness at the progressive stage and the number of people affected worldwide is expected to reach over 79 million by 2020. Currently, glaucoma management relies on pharmacological and invasive surgical treatments mainly by reducing the intraocular pressure (IOP), which is the most important risk factor for the progression of the visual field loss. Recent research suggests that neuroprotective or neuroregenerative approaches are necessary to prevent retinal ganglion cells (RGCs) loss and visual impairment over time. Neuroprotection is a new therapeutic strategy that attempts to keep RGCs alive and functional. New gene and cell therapeutics encoding neurotrophic factors (NTFs) are emerging for both neuroprotection and regenerative treatments for retinal diseases. This article briefly reviews the role of NTFs in glaucoma and the potential delivery systems.
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Affiliation(s)
- Nafiseh Nafissi
- School of Pharmacy and Waterloo Institute of Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada
| | - Marianna Foldvari
- School of Pharmacy and Waterloo Institute of Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada
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24
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Breger JC, Ancona MG, Walper SA, Oh E, Susumu K, Stewart MH, Deschamps JR, Medintz IL. Understanding How Nanoparticle Attachment Enhances Phosphotriesterase Kinetic Efficiency. ACS NANO 2015; 9:8491-503. [PMID: 26230391 DOI: 10.1021/acsnano.5b03459] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
As a specific example of the enhancement of enzymatic activity that can be induced by nanoparticles, we investigate the hydrolysis of the organophosphate paraoxon by phosphotriesterase (PTE) when the latter is displayed on semiconductor quantum dots (QDs). PTE conjugation to QDs underwent extensive characterization including structural simulations, electrophoretic mobility shift assays, and dynamic light scattering to confirm orientational and ratiometric control over enzyme display which appears to be necessary for enhancement. PTE hydrolytic activity was then examined when attached to ca. 4 and 9 nm diameter QDs in comparison to controls of freely diffusing enzyme alone. The results confirm that the activity of the QD conjugates significantly exceeded that of freely diffusing PTE in both initial rate (∼4-fold) and enzymatic efficiency (∼2-fold). To probe kinetic acceleration, various modified assays including those with increased temperature, presence of a competitive inhibitor, and increased viscosity were undertaken to measure the activation energy and dissociation rates. Cumulatively, the data indicate that the higher activity is due to an acceleration in enzyme-product dissociation that is presumably driven by the markedly different microenvironment of the PTE-QD bioconjugate's hydration layer. This report highlights how a specific change in an enzymatic mechanism can be both identified and directly linked to its enhanced activity when displayed on a nanoparticle. Moreover, the generality of the mechanism suggests that it could well be responsible for other examples of nanoparticle-enhanced catalysis.
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Affiliation(s)
- Joyce C Breger
- American Society for Engineering Education , Washington, DC 20036, United States
| | | | | | - Eunkeu Oh
- Sotera Defense Solutions, Inc. 7230 Lee DeForest Drive, Columbia, Maryland 21046, United States
| | - Kimihiro Susumu
- Sotera Defense Solutions, Inc. 7230 Lee DeForest Drive, Columbia, Maryland 21046, United States
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25
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Sun H, Chen H, Zang X, Hou P, Zhou B, Liu Y, Wu F, Cao X, Zhang X. Application of the Cre/loxP Site-Specific Recombination System for Gene Transformation in Aurantiochytrium limacinum. Molecules 2015; 20:10110-21. [PMID: 26039334 PMCID: PMC6272215 DOI: 10.3390/molecules200610110] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/08/2015] [Accepted: 05/21/2015] [Indexed: 12/14/2022] Open
Abstract
The Cre/loxP site-specific recombination system was applied to Aurantiochytrium limacinum to obtain a transformant without the antibiotic resistance marker gene. First, the enhanced green fluorescent protein gene (egfp) and chloramphenicol resistance gene (Cmr), along with the two loxP loci, were integrated into the genome of A. limacinum OUC88 using 18S rDNA sequences as the homologous recombination sites. Then plasmid pSH65, containing a zeocin resistance gene (Bler) was transferred into A. limacinum OUC_CG. After induction with galactose, repeated passage in culture and PCR-based assessment, the pSH65 plasmid was lost and A. limacinum OUC_EG host was shown to no longer have resistance to 100 mg chloramphenicol/L or 5 mg zeocin/L. Through southern blotting and fluorescence detection, egfp was found to be integrated into the genome of A. limacinum OUC_EG, and EGFP was successfully expressed in the cells. The successful application of the Cre/loxP system demonstrates an experimental basis for genetic modification of A. limacinum so as to obtain transformed strains with no antibiotic resistance marker genes.
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Affiliation(s)
- Hengyi Sun
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Hao Chen
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Xiaonan Zang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Pan Hou
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Bingbing Zhou
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Yuantao Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Fei Wu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Xiaofei Cao
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Xuecheng Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, China.
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26
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Siau JW, Chee S, Makhija H, Wai CMM, Chandra SHV, Peter S, Dröge P, Ghadessy FJ. Directed evolution of λ integrase activity and specificity by genetic derepression. Protein Eng Des Sel 2015; 28:211-20. [DOI: 10.1093/protein/gzv015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 02/20/2015] [Indexed: 12/18/2022] Open
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27
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Gaspar V, de Melo-Diogo D, Costa E, Moreira A, Queiroz J, Pichon C, Correia I, Sousa F. Minicircle DNA vectors for gene therapy: advances and applications. Expert Opin Biol Ther 2014; 15:353-79. [PMID: 25539147 DOI: 10.1517/14712598.2015.996544] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Nucleic-acid-based biopharmaceuticals enclose a remarkable potential for treating debilitating or life-threatening diseases that currently remain incurable. This promising area of research envisages the creation of state-of-the-art DNA vaccines, pluripotent cells or gene-based therapies, which can be used to overcome current issues. To achieve this goal, DNA minicircles are emerging as ideal nonviral vectors due to their safety and persistent transgene expression in either quiescent or actively dividing cells. AREAS COVERED This review focuses on the characteristics of minicircle DNA (mcDNA) technology and the current advances in their production. The possible modifications to further improve minicircle efficacy are also emphasized and discussed in light of recent advances. As a final point, the main therapeutic applications of mcDNA are summarized, with a special focus on pluripotent stem cells production and cancer therapy. EXPERT OPINION Achieving in-target and persistent transgene expression is a challenging issue that is of critical importance for a successful therapeutic outcome. The use of miniaturized mcDNA cassettes with additional modifications that increase and prolong expression may contribute to an improved generation of biopharmaceuticals. The unique features of mcDNA render it an attractive alternative to overcome current technical issues and to bridge the significant gap that exists between basic research and clinical applications.
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Affiliation(s)
- Vítor Gaspar
- University of Beira Interior, CICS-UBI - Health Sciences Research Center , Av. Infante D. Henrique, 6200-506, Covilhã , Portugal +351 275 329 002, +351 275 329 055 ; +351 275 329 099 ; ;
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The genomes, proteomes, and structures of three novel phages that infect the Bacillus cereus group and carry putative virulence factors. J Virol 2014; 88:11846-60. [PMID: 25100842 DOI: 10.1128/jvi.01364-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
This article reports the results of studying three novel bacteriophages, JL, Shanette, and Basilisk, which infect the pathogen Bacillus cereus and carry genes that may contribute to its pathogenesis. We analyzed host range and superinfection ability, mapped their genomes, and characterized phage structure by mass spectrometry and transmission electron microscopy (TEM). The JL and Shanette genomes were 96% similar and contained 217 open reading frames (ORFs) and 220 ORFs, respectively, while Basilisk has an unrelated genome containing 138 ORFs. Mass spectrometry revealed 23 phage particle proteins for JL and 15 for Basilisk, while only 11 and 4, respectively, were predicted to be present by sequence analysis. Structural protein homology to well-characterized phages suggested that JL and Shanette were members of the family Myoviridae, which was confirmed by TEM. The third phage, Basilisk, was similar only to uncharacterized phages and is an unrelated siphovirus. Cryogenic electron microscopy of this novel phage revealed a T=9 icosahedral capsid structure with the major capsid protein (MCP) likely having the same fold as bacteriophage HK97 MCP despite the lack of sequence similarity. Several putative virulence factors were encoded by these phage genomes, including TerC and TerD involved in tellurium resistance. Host range analysis of all three phages supports genetic transfer of such factors within the B. cereus group, including B. cereus, B. anthracis, and B. thuringiensis. This study provides a basis for understanding these three phages and other related phages as well as their contributions to the pathogenicity of B. cereus group bacteria. Importance: The Bacillus cereus group of bacteria contains several human and plant pathogens, including B. cereus, B. anthracis, and B. thuringiensis. Phages are intimately linked to the evolution of their bacterial hosts and often provide virulence factors, making the study of B. cereus phages important to understanding the evolution of pathogenic strains. Herein we provide the results of detailed study of three novel B. cereus phages, two highly related myoviruses (JL and Shanette) and an unrelated siphovirus (Basilisk). The detailed characterization of host range and superinfection, together with results of genomic, proteomic, and structural analyses, reveal several putative virulence factors as well as the ability of these phages to infect different pathogenic species.
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